from singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods import UmiBarcodeDemuxMethod

from singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods import DemultiplexingStrategy

from singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods import NonMultiplexable

from singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods import TaggedRecord

from singlecellmultiomics.modularDemultiplexer.baseDemultiplexMethods import TagDefinitions

import singlecellmultiomics.barcodeFileParser.barcodeFileParser as barcodeFileParser

class IlluminaBaseDemultiplexer(DemultiplexingStrategy):

    def __init__(

            self,

            indexFileParser,

            indexFileAlias='illumina_merged_ThruPlex48S_RP',

            **kwargs):

        self.barcodeFileParser = None

        DemultiplexingStrategy.__init__(self)

        self.indexFileParser = indexFileParser

        self.illuminaIndicesAlias = indexFileAlias

        self.shortName = 'ILLU'

        self.longName = 'IlluminaDemux'

        self.autoDetectable = False

        self.description = 'Demultiplex as a bulk sample'

        self.barcodeSummary = 'Bulk, no cell barcodes'

        self.indexSummary = f'sequencing indices: {indexFileAlias}'

    def demultiplex(self, records, library=None, reason=None, **kwargs):

        global TagDefinitions

        try:

            return [

                TaggedRecord(

                    rawRecord=record,

                    tagDefinitions=TagDefinitions,

                    indexFileParser=self.indexFileParser,

                    indexFileAlias=self.illuminaIndicesAlias,

                    library=library,

                    reason=reason) for record in records]

            #[TaggedRecord(rawRecord=record,tagDefinitions=TagDefinitions,indexFileParser=self.indexFileParser, indexFileAlias=self.illuminaIndicesAlias, library=library).asFastq(record.sequence, record.plus, record.qual) for record in records]

        except NonMultiplexable:

            raise

        except Exception as e:

            raise